Depression is identified as one of the most common psychiatric symptoms in Alzheimer's disease (AD). The comorbidity of AD and depression increases the burden of clinical treatment and care in elderly patients. In order to find new treatment options, we first proposed the dual RAGE/SERT inhibitors by fusing the key pharmacophore of vilazodone and azeliragon for the potential treatment of AD with comorbid depression. After a series of structural modifications, 34 dual-target directed ligands were designed and synthesized, and their RAGE and SERT inhibitory activities were systematically evaluated. Among them, compound 12 showed good dual-target bioactivities against RAGE (IC50 = 8.26 ± 1.12 μM) and SERT (IC50 = 31.09 ± 5.15 nM) in vitro, better safety profile than azeliragon, good liver microsomal stability, weak CYP inhibition, and acceptable pharmacokinetic properties. Moreover, 12 ameliorated Aβ25-35-induced neurotoxicity in SH-SY5Y cells and alleviated the depressive symptom in tail suspension test. In brief, these results indicated that 12 is a prospective prototype for the potential treatment of AD with comorbid depression. Display omitted •A novel therapeutic strategy of RAGE/SERT inhibitors for the treatment of AD with comorbid depression was firstly proposed.•Multiple vilazodone-azeliragon chimeric derivatives were designed, synthesized and evaluated as dual RAGE/SERT inhibitors.•Compound 12 showed good RAGE/SERT inhibitory activities and better safety profile than azeliragon.•Compound 12 exhibited significant neuroprotective effect against Aβ25-35-induced neuronal damage and alleviated depressive behavior of mice.